See it here.
This will help you create custom water colors and apply them to an individual world. OR, if you would like to make a package that affects all worlds, simply follow this tutorial, except import the ini files into a new empty file, and save it as a package.
It's pretty easy, but it takes a lot of tweaking to get the right colors. Note that you can edit the ini files while in-game and see results right away, so backup your ini files and edit them while playing. Then replace with the originals and create your custom package/world. :D